comparison variant_effect_predictor/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =cut
20
21 =head1 NAME
22
23 Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor - Facilitates DB storage and retrieval of compressed sequence
24
25 =head1 SYNOPSIS
26
27 $seq_adptr = $database_adaptor->get_SequenceAdaptor();
28
29 $dna =
30 ${ $seq_adptr->fetch_by_Slice_start_end_strand( $slice, 1, 1000,
31 -1 ) };
32
33 =head1 DESCRIPTION
34
35 An adaptor for the retrieval of compressed DNA sequence from the EnsEMBL
36 database
37
38 =head1 METHODS
39
40 =cut
41
42 package Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor;
43
44 use vars qw(@ISA);
45 use strict;
46
47 use Bio::EnsEMBL::DBSQL::SequenceAdaptor;
48
49 @ISA = qw(Bio::EnsEMBL::DBSQL::SequenceAdaptor);
50
51
52 sub _fetch_seq {
53 my $self = shift;
54 my $seq_region_id = shift;
55 my $start = shift;
56 my $len = shift;
57
58 #calculate the offset and start in the compressed sequence
59 my $comp_start = ($start-1 >> 2) + 1;
60 my $comp_len = ($len >> 2) + 2;
61
62 my ($bvector, $nline);
63
64 my $sth = $self->prepare(
65 "SELECT SUBSTRING( d.sequence, ?, ?), n_line
66 FROM dnac d
67 WHERE d.seq_region_id = ?");
68 $sth->bind_param(1,$comp_start,SQL_INTEGER);
69 $sth->bind_param(2,$comp_len ,SQL_INTEGER);
70 $sth->bind_param(3,$seq_region_id,SQL_INTEGER);
71 $sth->execute();
72 $sth->bind_columns(\$bvector, \$nline);
73 $sth->fetch();
74 $sth->finish();
75
76 #convert sequence from binary string to 0123 string
77 my $bitlen = length($bvector) << 2;
78 my $str = '';
79 for(my $i=0; $i < $bitlen; $i++) {
80 $str .= vec($bvector, $i, 2);
81 }
82
83 #convert from 0123 to ACTG
84 $str =~ tr/0123/ACTG/;
85
86 $str = substr($str, ($start-1)%4, $len);
87
88 #expand the nlines and place them back in the sequence
89 my @nlines = split(/:/, $nline);
90 foreach my $nl (@nlines) {
91 my ($offset,$char,$nlen) = $nl =~ /(\d+)(\D)(\d+)/;
92
93 #skip nlines entirely out of range
94 next if(($offset+$nlen-1) < $start || $offset > ($start+$len-1));
95
96 #obtain relative offset into requested region
97 $offset = $offset - $start + 1;
98
99 #nlines that partially overlap requested region have to be shrunk
100 if($offset < 1) {
101 $nlen = $nlen - (1-$offset);
102 $offset = 1;
103 }
104 if($offset + $nlen > $start+$len) {
105 $nlen = $len - $offset + 1;
106 }
107
108 substr($str,$offset-1,$nlen) = $char x $nlen;
109 }
110
111 return \$str;
112 }
113
114
115 =head2 store
116
117 Arg [1] : string $seq_region_id the id of the sequence region this dna
118 will be associated with.
119 Arg [2] : string reference $sequence the dna sequence to be stored in
120 the database
121 Example : $dbID = $seq_adaptor->store(12,\'ACTGGGTACCAAACAAACACAACA');
122 Description: stores a dna sequence in the databases dna table and returns the
123 database identifier for the new record.
124 Returntype : int
125 Exceptions : none
126 Caller : Bio::EnsEMBL::DBSQL::RawContigAdaptor::store
127 Status : Stable
128
129 =cut
130
131 sub store {
132 my ($self, $seq_region_id, $sequence) = @_;
133
134 if(!$seq_region_id) {
135 throw('seq_region_id is required');
136 }
137
138 $sequence = uc($sequence);
139
140 my $bvector = '';
141
142 #convert sequence to 0s,1s,2s and 3s
143 $sequence =~ tr/ACTG/0123/;
144
145 #nlines cover sequence which is not ACTG such as N
146 #nline format is a set of colon delimited int, char, int triplets:
147 #<offset><code><length>
148 my($nline_char,$nline_len,$nline_off);
149 my @nlines;
150
151 my $len = length($sequence);
152 for(my $i=0; $i < $len; $i++) {
153 my $char = substr($sequence,$i,1);
154
155 #quickly check if this character was an A,C,T or G (and was converted to
156 # a 0,1,2,3)
157 if($char =~ /[0-3]/) {
158 vec($bvector, $i,2) = $char;
159 if($nline_char) {
160 #end of an nline
161 push @nlines, "$nline_off$nline_char$nline_len";
162 $nline_char = undef;
163 $nline_len = 0;
164 $nline_off = 0;
165 }
166 } else {
167 #this was not an ACTG
168 if($nline_char) {
169 if($nline_char eq $char) {
170 #continuation of an nline
171 $nline_len++;
172 } else {
173 #end of a previous nline and start of a new one
174 push @nlines, "$nline_off$nline_char$nline_len";
175 $nline_char = $char;
176 $nline_len = 1;
177 $nline_off = $i+1;
178 }
179 } else {
180 #start of a new nline
181 $nline_char = $char;
182 $nline_len = 1;
183 $nline_off = $i+1;
184 }
185 $char = 0; #need to put numeric val into bitvector despite nline
186 }
187
188 vec($bvector, $i,2) = $char;
189 }
190
191 my $nline = join(':', @nlines);
192 my $statement = $self->prepare(
193 "INSERT INTO dnac(seq_region_id, sequence, n_line) VALUES(?,?,?)");
194
195 $statement->bind_param(1,$seq_region_id,SQL_INTEGER);
196 $statement->bind_param(2,$bvector,SQL_BLOB);
197 $statement->bind_param(3,$nline,SQL_LONGVARCHAR);
198 $statement->execute();
199
200 $statement->finish();
201 return;
202 }
203
204
205 1;